Multiplexed affinity-based screening is widespread in biology, whereby potential biomolecular candidates in a sample pool are screened against capturing biomolecules immobilized on an array surface. For example, DNA microarrays enable the massively parallel screening of sample RNA that may hybridize to any of thousands of gene sequences arrayed on a surface. It is often useful to recover the bound biomolecule species afterwards for complete identification (e.g. DNA sequencing) and to generate more copies (e.g. PCR amplification), particularly if the original sample pool is a priori unknown. One such instance is the identification of previously uncharacterized corona viruses such as SARS, whereby viral nucleic acids hybridized to a DNA microarray were individually scraped off using tungsten needles for PCR [1]. Although this approach is simple, its disadvantages include contamination, loss and destruction of samples.
Current technologies fail to combine both multiplexed affinity-based screening and sample recovery. Whatman's FTA® Elute have been used to recover total DNA without specificity from whole blood or buccal cheek cells [2-5]. HPLC systems allow for affinity-based screening and sample recovery, but multiple columns and the systems can be prohibitively expensive. Microfluidic systems have had some early success at addressing these problems. For example, nucleic acid aptamers that showed binding to protein have been selected from a sample library pool and recovered using heating electrodes [6] or micromagnetic beads [7]. The challenge remains to reliably isolate and individually recover biomolecule species of interest after multiplexed screening.
Aptamers are short length nucleic acids that bind to proteins, and are emerging as potential therapeutic molecules that could target proteins involved in disease. Systematic evolution of ligands by exponential enrichment (SELEX) is a process utilized to select aptamers with high affinity binding to proteins. SELEX requires both affinity-based screening and subsequent recovery of aptamers that bind to proteins for PCR amplification. With each cycle of SELEX, the stringency of binding in the screening process is increased, and at the end of several SELEX rounds, aptamers with high binding affinity are systematically evolved. SELEX is time consuming and microfluidics have been shown to shorten the process [7-9]. However these microfluidic systems involve selection against one protein at a time; it would be desirable to develop a microfluidic system or other technologies capable of multiplexed selection and screening simultaneously.
The present invention is directed to overcoming these and other deficiencies in the art.